HEADER PROTEIN BINDING 25-AUG-10 3OKQ TITLE CRYSTAL STRUCTURE OF A CORE DOMAIN OF YEAST ACTIN NUCLEATION COFACTOR TITLE 2 BUD6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BUD SITE SELECTION PROTEIN 6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: COILED-COIL DOMAIN (UNP RESIDUES 549-688); COMPND 5 SYNONYM: ACTIN-INTERACTING PROTEIN 3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BREWER'S YEAST,LAGER BEER YEAST,YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: AIP3, BUD6, L8543.5, YLR319C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30 KEYWDS COILED-COIL, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR D.TU,M.J.ECK REVDAT 4 06-SEP-23 3OKQ 1 SEQADV REVDAT 3 26-DEC-12 3OKQ 1 JRNL REVDAT 2 05-DEC-12 3OKQ 1 JRNL REVDAT 1 14-SEP-11 3OKQ 0 JRNL AUTH D.TU,B.R.GRAZIANO,E.PARK,W.ZHENG,Y.LI,B.L.GOODE,M.J.ECK JRNL TITL STRUCTURE OF THE FORMIN-INTERACTION DOMAIN OF THE ACTIN JRNL TITL 2 NUCLEATION-PROMOTING FACTOR BUD6. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 E3424 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 23161908 JRNL DOI 10.1073/PNAS.1203035109 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 12848 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.490 REMARK 3 FREE R VALUE TEST SET COUNT : 962 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 35.3988 - 3.9081 0.99 1768 154 0.2088 0.2312 REMARK 3 2 3.9081 - 3.1025 1.00 1717 135 0.1823 0.2206 REMARK 3 3 3.1025 - 2.7105 1.00 1715 132 0.1934 0.2333 REMARK 3 4 2.7105 - 2.4627 1.00 1707 129 0.1811 0.2155 REMARK 3 5 2.4627 - 2.2863 1.00 1682 133 0.1810 0.2193 REMARK 3 6 2.2863 - 2.1515 1.00 1672 141 0.1736 0.2437 REMARK 3 7 2.1515 - 2.0438 0.97 1625 138 0.1925 0.2091 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 42.51 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 13.85200 REMARK 3 B22 (A**2) : -10.87840 REMARK 3 B33 (A**2) : -2.97360 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1027 REMARK 3 ANGLE : 0.881 1378 REMARK 3 CHIRALITY : 0.056 160 REMARK 3 PLANARITY : 0.003 176 REMARK 3 DIHEDRAL : 15.493 406 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3OKQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000061238. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : MD2 MICRODIFFRACTOMETER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12868 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3ONX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 3350, 175 MM SODIUM MALONATE REMARK 280 (PH 7.0), 20% GLYCEROL, 5 MM DTT, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.39350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.39350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 29.44150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.60700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.44150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.60700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 35.39350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.44150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.60700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 35.39350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.44150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.60700 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 548 REMARK 465 SER A 549 REMARK 465 ALA A 550 REMARK 465 LYS A 551 REMARK 465 ASN A 552 REMARK 465 GLU A 678 REMARK 465 GLU A 679 REMARK 465 GLN A 680 REMARK 465 GLU A 681 REMARK 465 LYS A 682 REMARK 465 ASN A 683 REMARK 465 PRO A 684 REMARK 465 SER A 685 REMARK 465 ARG A 686 REMARK 465 SER A 687 REMARK 465 LYS A 688 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ONX RELATED DB: PDB DBREF 3OKQ A 549 688 UNP P41697 BUD6_YEAST 549 688 SEQADV 3OKQ GLY A 548 UNP P41697 EXPRESSION TAG SEQRES 1 A 141 GLY SER ALA LYS ASN SER SER ASN ARG MET TYR MET GLU SEQRES 2 A 141 LYS SER GLN THR GLU LEU GLY ASP LEU SER ASP THR LEU SEQRES 3 A 141 LEU SER LYS VAL ASP ASP LEU GLN ASP VAL ILE GLU ILE SEQRES 4 A 141 MET ARG LYS ASP VAL ALA GLU ARG ARG SER GLN PRO ALA SEQRES 5 A 141 LYS LYS LYS LEU GLU THR VAL SER LYS ASP LEU GLU ASN SEQRES 6 A 141 ALA GLN ALA ASP VAL LEU LYS LEU GLN GLU PHE ILE ASP SEQRES 7 A 141 THR GLU LYS PRO HIS TRP LYS LYS THR TRP GLU ALA GLU SEQRES 8 A 141 LEU ASP LYS VAL CYS GLU GLU GLN GLN PHE LEU THR LEU SEQRES 9 A 141 GLN GLU GLU LEU ILE LEU ASP LEU LYS GLU ASP LEU GLY SEQRES 10 A 141 LYS ALA LEU GLU THR PHE ASP LEU ILE LYS LEU CYS CYS SEQRES 11 A 141 GLU GLU GLN GLU LYS ASN PRO SER ARG SER LYS FORMUL 2 HOH *127(H2 O) HELIX 1 1 SER A 554 ARG A 595 1 42 HELIX 2 2 ALA A 599 CYS A 677 1 79 CRYST1 58.883 95.214 70.787 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016983 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010503 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014127 0.00000